--- trunk/src/rnemd/RNEMD.cpp	2012/08/22 02:28:28	1782
+++ trunk/src/rnemd/RNEMD.cpp	2012/08/31 21:16:10	1793
@@ -53,6 +53,11 @@
 #include <mpi.h>
 #endif
 
+#ifdef _MSC_VER
+#define isnan(x) _isnan((x))
+#define isinf(x) (!_finite(x) && !_isnan(x))
+#endif
+
 #define HONKING_LARGE_VALUE 1.0e10
 
 using namespace std;
@@ -65,7 +70,6 @@ namespace OpenMD {
     failTrialCount_ = 0;
     failRootCount_ = 0;
 
-    int seedValue;
     Globals * simParams = info->getSimParams();
     RNEMDParameters* rnemdParams = simParams->getRNEMDParameters();
 
@@ -305,7 +309,7 @@ namespace OpenMD {
     z.title =  "Z";
     z.dataType = "RealType";
     z.accumulator.reserve(nBins_);
-    for (unsigned int i = 0; i < nBins_; i++) 
+    for (int i = 0; i < nBins_; i++) 
       z.accumulator.push_back( new Accumulator() );
     data_[Z] = z;
     outputMap_["Z"] =  Z;
@@ -315,7 +319,7 @@ namespace OpenMD {
     temperature.title =  "Temperature";
     temperature.dataType = "RealType";
     temperature.accumulator.reserve(nBins_);
-    for (unsigned int i = 0; i < nBins_; i++) 
+    for (int i = 0; i < nBins_; i++) 
       temperature.accumulator.push_back( new Accumulator() );
     data_[TEMPERATURE] = temperature;
     outputMap_["TEMPERATURE"] =  TEMPERATURE;
@@ -325,7 +329,7 @@ namespace OpenMD {
     velocity.title =  "Velocity";  
     velocity.dataType = "Vector3d";
     velocity.accumulator.reserve(nBins_);
-    for (unsigned int i = 0; i < nBins_; i++) 
+    for (int i = 0; i < nBins_; i++) 
       velocity.accumulator.push_back( new VectorAccumulator() );
     data_[VELOCITY] = velocity;
     outputMap_["VELOCITY"] = VELOCITY;
@@ -335,7 +339,7 @@ namespace OpenMD {
     density.title =  "Density";
     density.dataType = "RealType";
     density.accumulator.reserve(nBins_);
-    for (unsigned int i = 0; i < nBins_; i++) 
+    for (int i = 0; i < nBins_; i++) 
       density.accumulator.push_back( new Accumulator() );
     data_[DENSITY] = density;
     outputMap_["DENSITY"] =  DENSITY;
@@ -447,7 +451,6 @@ namespace OpenMD {
 
     int selei;
     StuntDouble* sd;
-    int idx;
 
     RealType min_val;
     bool min_found = false;   
@@ -460,8 +463,6 @@ namespace OpenMD {
     for (sd = seleMan_.beginSelected(selei); sd != NULL; 
          sd = seleMan_.nextSelected(selei)) {
 
-      idx = sd->getLocalIndex();
-
       Vector3d pos = sd->getPos();
 
       // wrap the stuntdouble's position back into the box:
@@ -539,12 +540,9 @@ namespace OpenMD {
       }
     }
     
-#ifdef IS_MPI
-    int nProc, worldRank;
+#ifdef IS_MPI    
+    int worldRank = MPI::COMM_WORLD.Get_rank();
     
-    nProc = MPI::COMM_WORLD.Get_size();
-    worldRank = MPI::COMM_WORLD.Get_rank();
-
     bool my_min_found = min_found;
     bool my_max_found = max_found;
 
@@ -777,7 +775,6 @@ namespace OpenMD {
 
     int selei;
     StuntDouble* sd;
-    int idx;
 
     vector<StuntDouble*> hotBin, coldBin;
 
@@ -799,8 +796,6 @@ namespace OpenMD {
     for (sd = seleMan_.beginSelected(selei); sd != NULL; 
          sd = seleMan_.nextSelected(selei)) {
 
-      idx = sd->getLocalIndex();
-
       Vector3d pos = sd->getPos();
 
       // wrap the stuntdouble's position back into the box:
@@ -1227,7 +1222,6 @@ namespace OpenMD {
 
     int selei;
     StuntDouble* sd;
-    int idx;
 
     vector<StuntDouble*> hotBin, coldBin;
 
@@ -1242,8 +1236,6 @@ namespace OpenMD {
     for (sd = seleMan_.beginSelected(selei); sd != NULL; 
          sd = seleMan_.nextSelected(selei)) {
 
-      idx = sd->getLocalIndex();
-
       Vector3d pos = sd->getPos();
 
       // wrap the stuntdouble's position back into the box:
@@ -1425,7 +1417,6 @@ namespace OpenMD {
 
     int selei;
     StuntDouble* sd;
-    int idx;
 
     vector<RealType> binMass(nBins_, 0.0);
     vector<RealType> binPx(nBins_, 0.0);
@@ -1450,10 +1441,8 @@ namespace OpenMD {
              sd = mol->nextIntegrableObject(iiter))
     */
     for (sd = seleMan_.beginSelected(selei); sd != NULL; 
-         sd = seleMan_.nextSelected(selei)) {
+         sd = seleMan_.nextSelected(selei)) {     
       
-      idx = sd->getLocalIndex();
-      
       Vector3d pos = sd->getPos();
 
       // wrap the stuntdouble's position back into the box:
@@ -1537,16 +1526,16 @@ namespace OpenMD {
         if(outputMask_[j]) {
           switch(j) {
           case Z:
-            (data_[j].accumulator[i])->add(z);
+            dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(z);
             break;
           case TEMPERATURE:
-            data_[j].accumulator[i]->add(temp);
+            dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(temp);
             break;
           case VELOCITY:
             dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
             break;
           case DENSITY:
-            data_[j].accumulator[i]->add(den);
+            dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(den);
             break;
           }
         }
@@ -1681,7 +1670,7 @@ namespace OpenMD {
       
       rnemdFile_.precision(8);
       
-      for (unsigned int j = 0; j < nBins_; j++) {        
+      for (int j = 0; j < nBins_; j++) {        
         
         for (unsigned int i = 0; i < outputMask_.size(); ++i) {
           if (outputMask_[i]) {
@@ -1707,7 +1696,7 @@ namespace OpenMD {
       rnemdFile_ << "#######################################################\n";
 
 
-      for (unsigned int j = 0; j < nBins_; j++) {        
+      for (int j = 0; j < nBins_; j++) {        
         rnemdFile_ << "#";
         for (unsigned int i = 0; i < outputMask_.size(); ++i) {
           if (outputMask_[i]) {
@@ -1743,7 +1732,7 @@ namespace OpenMD {
     assert(bin < nBins_);
     RealType s;
     
-    data_[index].accumulator[bin]->getAverage(s);
+    dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getAverage(s);
     
     if (! isinf(s) && ! isnan(s)) {
       rnemdFile_ << "\t" << s;
@@ -1781,7 +1770,7 @@ namespace OpenMD {
     assert(bin < nBins_);
     RealType s;
     
-    data_[index].accumulator[bin]->getStdDev(s);
+    dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getStdDev(s);
     
     if (! isinf(s) && ! isnan(s)) {
       rnemdFile_ << "\t" << s;